VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Feb 12 2015 - 19:29:53 CST

Thank you everyone. When "" used, atomselect worked. However now I am
getting a different error. My task is to randomly select a water molecule
from a dcd file and write their coordinates to a new pdb file. I used the
following script.

set random [expr round(rand()*100)]
set sel [atomselect top "resid $random"]
$sel writepdb out.pdb
$sel delete

I am getting an error saying; atomsel: frame -1 out of range for molecule 1

Can you please suggest a solution?

Thanks
Monika

On Thu, Feb 12, 2015 at 2:53 PM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:

> That will select every resid 5 from all the segments in your structure.
> The keyword you're looking for is "residue" (or, if you like, "segname XXX
> and resid 5").
>
>
>
> Tristan Croll
> Lecturer
> Faculty of Health
> School of Biomedical Sciences
> Institute of Health and Biomedical Engineering
> Queensland University of Technology
> 60 Musk Ave
> Kelvin Grove QLD 4059 Australia
> +61 7 3138 6443
>
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>
> > On 12 Feb 2015, at 5:44 pm, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
> >
> > Dear all,
> >
> > I need to select all the atoms of a particular water molecule from a dcd
> file and write it's coordinates to a separate pdb/dcd file. Can I do this
> using atomselect in vmd tcl? I tried the following command but it doesn't
> work.
> >
> > set sel [atomselect top {resid 5}]
> >
> > Thank you.
> > Monika
> >
> > --
> > W.A.Monika Madhavi
> > Lecturer (Probation),
> > Department of Physics,
> > University of Colombo.
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.